[Mesa-users] Help regarding MESA in a HPC

[Warrick Ball]

Hi Abhijnan,

Is there any public documentation for your cluster that you can point to, from which I can try to create a more detailed answer?

As Susmita says, you should install MESA and the SDK in the same way as a standard Linux installation, all executed on whatever cluster node you can interact with.  The caveat is that you may need to get to the SDK and MESA prerequisites differently.  For example, many clusters use environment modules to provide different versions of various software libraries, so you might have to load some modules for the SDK to intialise properly.  In this case, take note of which modules you need because you'll need to load them every time you initialise the SDK (with `mesasdk_init.sh`), including in your run scripts.

Regarding the submission script, I would personally include the environment information like OMP_NUM_THREADS directly in the script that you run.  So you might have a script file `mesa.pbs` with contents like

     # PBS directives
     module load ...
     export MESASDK_ROOT=...
     export MESA_DIR=...
     export OMP_NUM_THREADS=... # make sure this matches the PBS directives

     ./rn

but it's equally fine to do as Susmita suggests and have something like

     # PBS directives
     ./cluster.sh

and then have a script `cluster.sh` that has the module loads, exports and `./rn`.  My PBS knowledge is a bit shaky but hopefully this conveys the idea and the appropriate documentation will advise what you should fill in.

A few more cluster tips:

- Be aware that your default home folder might not have enough space for MESA in it (ours don't!), so you may need to consult your cluster documentation for the most appropriate place to install MESA.

- The build itself might need to be done in a PBS script if the admins prevent users from running long-running programs on the login nodes.

I hope that helps!

Regards,
Warrick

___________

Warrick Ball
Senior Research Software Engineer
University of Birmingham
W.H.Ball at bham.ac.uk

On Thu, 12 Sep 2024, ABHIJNAN KAR 20064 wrote:

> CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe.
> Hi users, I am trying to set up mesa in a cluster ( HPC) environment for the first time. I am new to handling clusters through terminal. I am wondering as to whether I should install MESA again on cluster or i can directly transfer the MESA
> directory/folder from my local computer to the cluster account ( along with mesasdk)? Also, for the running script of mesa ( which includes setting the no of threads, setting a path for mesasdk etc), should I mention those in pbs job script itself?
> It would be really helpful, if this can be sorted out.
> Regards,
> Abhijnan Kar(He/his/him)
> BS-MS,IISER Berhampur
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